Due to the limited depth of field of brightfield microscopes, it is usually impossible to image thick specimens entirely in focus. By optically sectioning the specimen, the in-focus information at the specimen''s surface can be acquired over a range of images. Commonly based on a high-pass criterion, extended-depth-of-field methods aim at combining the in-focus information from these images into a single image of the texture on the specimen''s surface. The topography provided by such methods is usually limited to a map of selected in-focus pixel positions and is inherently discretized along the axial direction, which limits its use for quantitative evaluation. In this paper, we propose a method that jointly estimates the texture and topography of a specimen from a series of brightfield optical sections; it is based on an image formation model that is described by the convolution of a thick specimen model with the microscope''s point spread function. The problem is stated as a least-squares minimization where the texture and topography are updated alternately. This method also acts as a deconvolution when the in-focus PSF has a blurring effect, or when the true in-focus position falls in between two optical sections. Comparisons to state-of-the-art algorithms and experimental results demonstrate the potential of the proposed approach.
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